Class: Bio::KEGG::DRUG

Inherits:

Bio::KEGGDB

• Object
• DB
• NCBIDB
• Bio::KEGGDB
• Bio::KEGG::DRUG

show all

Includes:

Common::DblinksAsHash, Common::PathwaysAsHash

Defined in:

lib/bio/db/kegg/drug.rb

Overview

Constant Summary

DELIMITER =

RS = "\n///\n"

TAGSIZE =

12

Instance Method Summary (collapse)

• - (Object) activity

  Biological or chemical activity described in the ACTIVITY line.

• - (Object) comment

  COMMENT lines.

• - (Object) dblinks_as_hash (also: #dblinks)
• - (Object) dblinks_as_strings

  List of database names and IDs, described in the DBLINKS lines.

• - (Object) entry_id

  ID of the entry, described in the ENTRY line.

• - (Object) formula

  Chemical formula described in the FORMULA line.

• - (DRUG) initialize(entry) constructor

  Creates a new Bio::KEGG::DRUG object.

• - (Object) kcf

  ATOM, BOND lines.

• - (Object) mass

  Molecular weight described in the MASS line.

• - (Object) name

  The first name recorded in the NAME field.

• - (Object) names

  Names described in the NAME line.

• - (Object) pathways_as_hash (also: #pathways)
• - (Object) pathways_as_strings

  List of KEGG Pathway IDs with short descriptions, described in the PATHWAY lines.

• - (Object) products

  Product names described in the PRODUCTS lines.

• - (Object) remark

  REMARK lines.

Methods inherited from DB

#exists?, #fetch, #get, open, #tags

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# File 'lib/bio/db/kegg/drug.rb', line 45

def initialize(entry)
  super(entry, TAGSIZE)
end

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# File 'lib/bio/db/kegg/drug.rb', line 87

def activity
  field_fetch('ACTIVITY')
end

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# File 'lib/bio/db/kegg/drug.rb', line 123

def comment
  field_fetch('COMMENT')
end

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# File 'lib/bio/db/kegg/drug.rb', line 32

def dblinks_as_hash; super; end

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# File 'lib/bio/db/kegg/drug.rb', line 109

def dblinks_as_strings
  lines_fetch('DBLINKS')
end

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# File 'lib/bio/db/kegg/drug.rb', line 52

def entry_id
  field_fetch('ENTRY')[/\S+/]
end

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# File 'lib/bio/db/kegg/drug.rb', line 73

def formula
  field_fetch('FORMULA')
end

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# File 'lib/bio/db/kegg/drug.rb', line 116

def kcf
  return "#{get('ATOM')}#{get('BOND')}"
end

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# File 'lib/bio/db/kegg/drug.rb', line 80

def mass
  field_fetch('MASS').to_f
end

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# File 'lib/bio/db/kegg/drug.rb', line 66

def name
  names.first
end

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# File 'lib/bio/db/kegg/drug.rb', line 59

def names
  field_fetch('NAME').split(/\s*;\s*/)
end

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# File 'lib/bio/db/kegg/drug.rb', line 37

def pathways_as_hash; super; end

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# File 'lib/bio/db/kegg/drug.rb', line 102

def pathways_as_strings
  lines_fetch('PATHWAY') 
end

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# File 'lib/bio/db/kegg/drug.rb', line 130

def products
  lines_fetch('PRODUCTS')
end

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# File 'lib/bio/db/kegg/drug.rb', line 94

def remark
  field_fetch('REMARK')
end